Loose drummer

The members of my band are good musicians, even my drummer is creative, but he plays loose--at least to the other three members' ears. When I say loose, I mean he loses time on some (about 2/3) of his fills, but he can keep a straight beat. His high-hat will usually stay straight through the bad fills, and he can keep damn good time with a metronome but his tom work is lack-luster at best. I'm afraid he's all we've got for now so getting rid of him is not really an option. He's also a long time friend.
Anyway I am currently using a three mic set-up: two OH and a kick mic. My question is: Will micing every drum make this easier to edit (Cakewalk Pro 9.0)? Will it still be easy considering the possible phase problems my green ass will almost certainly incur?

No miking combination will really save you from poor meter. You can mic everything close and gate, and edit like crazy, but you will always end up with a track that sounds whacked. One thing you can try is punching in the fills (made much easier by being able to fine tune your edit points after you do the punch), or copying another section where he does the same fill, but in-time.
Convince him to practice with a metronome. Doing the fill (and the lead-in and lead-out parts) to a click track for a couple of hours will iron it out. Doc

I think Doc has the right idea- as long as the drummer will go along with it. Have him play through the entire song, just doing the main rhythm part. You may even mix the rest of the band in to that, then have him add the fills as an overdub. If the song repeats the same fill, you might even find you can pick the best one, and just paste copies of it in each time it repeats. Not having to deal with the fills in real time will also allow the drummer to focus on the meter during the initial take.

one of the things you can do is get the drummere to try to fix his own mistakes while editing, after his brain explodes from frustration of not getting clean results with that mic configuration he can focus on the wonky sections.

the biggest problem of getting musicians to play in time is the realisation that there is a problem.

for me the thing that made the biggest difference in my playing over the years is getting to listen to myself with a click, where i have tendences to rush or drag.

having the ability to subdivide the fills, ie: count them out and know what note value the notes are supposed to be can be very helpfull as well.

if you can, if you know that the fill is say 16th notes, create a click that plays a 16th note subdivision at that bar in the tune to try to keep him on track.

these timing issues probably come from not feeling the time center while playing fills.